Customized phenotype association (ZS11)
Note that although accession names overlap with those in the database, the seed stocks might be sourced from different origins with potentially different degrees of purity, or maintained in different collections with the possibility of outcrossing, which lead to an unreliable result.
result(s) found in BnIR.
Basic information of gene(s)
| ZS11 ID | Darmor ID | AtGI/Name | Position | Seq/Exp/JBR | SNPs No. | SNP No.(High/Moderate/Low/Modifer) | SV No. | SV No.(INS/DEL) | Multi-locus selector |
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Phylogenetic tree, gene structure and variation distribution
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Define the upstream and downstream of gene
Choose flanking regions of gene to show.
Gene structure and SNP distribution
The inverted triangle symbols indicate variations, click it to see detailed information in table.
| Chr. | Position | Alt (allele) | Ref (allele) | JBrowser | Alt (frequency) | Ref (frequency) | PIC | Alt (num) | Ref (num) | Function type | Variation type | Functional annotations |
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Annotation and statistics of SNPs
Haplotype in and its ± 0 kb flanking region
PIC: polymorphism information content
| Chr. | Position | Alt (allele) | Ref (allele) | JBrowser | Alt (frequency) | Ref (frequency) | PIC | Alt (num) | Ref (num) | Function type | Variation type | Functional annotations |
|---|
Information of Haplotypes in and its ± 0 kb flanking region
According to the gene/region you input, we extract haplotype information. Note that selected frequency all exceed 0.010. And heterozygous and missing records have been filtered out.
| ID | Haplotype | Frequency | Sample |
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Customized phenotype
| select | trait |
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p-value:(Anova)
Allele frequency of haplotype in Subpopulation
According to the haplotype you submit, the chart shows the proportion of each sub-population in the haplotypes. hap_i(n) means the no.i haplotype had n pieces of material.
Geographic distribution of haplotypes in
According to the haplotype you submit, the chart shows the proportion of haplotypes in different continents. hap_i(n) means the no.i haplotype had n pieces of material.
Expression of
According to the haplotype you submit, the chart shows the expression level of haplotypes.
p-value:(Anova)
Information of SNPs in and its ± 0 kb flanking region
PIC: polymorphism information content
| Selector | Chr. | Position | Alt (allele) | Ref (allele) | JBrowser | Alt (frequency) | Ref (frequency) | PIC | Alt (num) | Ref (num) | Function type | Variation type | Functional annotations |
|---|
Customized phenotype
| Selector | Trait |
|---|
p-value: (t-test);
Allele frequency of in Subpopulation
Geographical distribution of
Expression of
p-value: (t-test); (wilcoxon-test)
Define the upstream and downstream of gene
Choose flanking region of gene to show.
Gene structure and SV distribution
The inverted triangle symbols indicate variations, click it to see detailed information in table.
SV information in and its ± kb flanking region
| Selector | Chr. | Start | End | ID | Len | Ref | Alt | Freq | JBrowser |
|---|
Customize phenotype
| Selector | Trait |
|---|
p-value: (t-test); (wilcoxon-test)
SV frequency of in subpopulation
Geographical distribution map of
Expression of
p-value: (t-test); (wilcoxon-test)
BnIR is developed by the Yanglab at Huazhong Agricultural University.
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